scholarly journals From sequences to enzymes: comparative genomics to study evolutionary conserved protein functions in marine microbes

2021 ◽  
Author(s):  
Angelina Cordone ◽  
Alessandro Coppola ◽  
Angelica Severino ◽  
Monica Correggia ◽  
Matteo Selci ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Evolutionary History ◽  
Life Forms ◽  
Research Field ◽  
Evolutionary Information ◽  
Marine Microorganisms ◽  
Marine Microbes ◽  
Evolutionary Changes ◽  
Protein Functions ◽  
Insight Into

Comparative genomics is a research field that allows comparison between genomes of different life forms providing information on the organization of the compared genomes, both in terms of structure and encoded functions. Moreover, this approach provides apowerful tool to study and understand the evolutionary changes and adaptation among organisms. Comparative genomics can be used to compare phylogenetically close marine organisms showing different vital strategies and lifestyles and obtain information regarding specific adaptations and/or their evolutionary history. Here we report a basic comparative genomics protocol to extrapolate evolutionary information about a protein of interest conserved across diverse marine microbes. The outlined approach can be used in a number of different settings and might help to gain new insight into the evolution and adaptation of marine microorganisms.

Green Synthesized Nanomaterials as Theranostic Platforms for Cancer Treatment: Principles, Challenges and the Road Ahead

2019 ◽  
Vol 26 (8) ◽  
pp. 1311-1327 ◽  
Author(s):  
Pala Rajasekharreddy ◽  
Chao Huang ◽  
Siddhardha Busi ◽  
Jobina Rajkumari ◽  
Ming-Hong Tai ◽  
...  
Keyword(s):  
Nanoparticle Synthesis ◽  
Research Field ◽  
Synthesis Methods ◽  
Synthetic Approach ◽  
Future Directions ◽  
The Road ◽  
New Methods ◽  
Recent Developments ◽  
Theranostic Applications ◽  
Insight Into

With the emergence of nanotechnology, new methods have been developed for engineering various nanoparticles for biomedical applications. Nanotheranostics is a burgeoning research field with tremendous prospects for the improvement of diagnosis and treatment of various cancers. However, the development of biocompatible and efficient drug/gene delivery theranostic systems still remains a challenge. Green synthetic approach of nanoparticles with low capital and operating expenses, reduced environmental pollution and better biocompatibility and stability is a latest and novel field, which is advantageous over chemical or physical nanoparticle synthesis methods. In this article, we summarize the recent research progresses related to green synthesized nanoparticles for cancer theranostic applications, and we also conclude with a look at the current challenges and insight into the future directions based on recent developments in these areas.

Empathy as moderator of gender differences in Chinese insurance agents' business ethical sensitivity

2017 ◽  
Vol 45 (6) ◽  
pp. 1029-1042 ◽  
Author(s):  
Na Zhang ◽  
Jian Zhang ◽  
Jing Wang
Keyword(s):  
Gender Differences ◽  
Business Ethics ◽  
Research Field ◽  
Ethical Sensitivity ◽  
Men And Women ◽  
Insurance Agents ◽  
Factors Associated ◽  
Ethics Research ◽  
The Relationship ◽  
Insight Into

To expand the business ethics research field, and to increase society's understanding of Chinese insurance agents' business ethics, we investigated how gender differences are related to agents' business ethical sensitivity and whether or not these relationships are moderated by empathy. Through a regression analysis of the factors associated with the business ethical sensitivity of 417 Chinese insurance agents, we found that gender played an important role in affecting business ethical sensitivity, and empathy significantly affected business ethical sensitivity. Furthermore, empathy had a moderating effect on the relationship between gender and business ethical sensitivity. Both men and women with strong empathy scored high on business ethical sensitivity; however, men with strong empathy had higher levels of business ethical sensitivity than did women with little empathy. The findings add to the literature by providing insight into the mechanisms responsible for the benefits of empathy in increasing business ethical sensitivity.

scholarly journals Relaxed Substrate Specificity in Qβ Replicase through Long-Term In Vitro Evolution

Life ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 32
Author(s):  
Kohtoh Yukawa ◽  
Ryo Mizuuchi ◽  
Norikazu Ichihashi
Keyword(s):  
Substrate Specificity ◽  
Early Life ◽  
Evolutionary History ◽  
Rna Replication ◽  
Life Forms ◽  
In Vitro Evolution ◽  
Present Evidence ◽  
Major Transition

A change from RNA- to DNA-based genetic systems is hypothesized as a major transition in the evolution of early life forms. One of the possible requirements for this transition is a change in the substrate specificity of the replication enzyme. It is largely unknown how such changes would have occurred during early evolutionary history. In this study, we present evidence that an RNA replication enzyme that has evolved in the absence of deoxyribonucleotide triphosphates (dNTPs) relaxes its substrate specificity and incorporates labeled dNTPs. This result implies that ancient replication enzymes, which probably evolved in the absence of dNTPs, could have incorporated dNTPs to synthesize DNA soon after dNTPs became available. The transition from RNA to DNA, therefore, might have been easier than previously thought.

scholarly journals Bichir external gills arise via heterochronic shift that accelerates hyoid arch development

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Jan Stundl ◽  
Anna Pospisilova ◽  
David Jandzik ◽  
Peter Fabian ◽  
Barbora Dobiasova ◽  
...  
Keyword(s):  
Pharyngeal Arch ◽  
Developmental Sequence ◽  
Free Living ◽  
Pharyngeal Arches ◽  
Hyoid Arch ◽  
Early Appearance ◽  
Evolutionary Changes ◽  
Insight Into ◽  
Living Group ◽  
Early Larvae

In most vertebrates, pharyngeal arches form in a stereotypic anterior-to-posterior progression. To gain insight into the mechanisms underlying evolutionary changes in pharyngeal arch development, here we investigate embryos and larvae of bichirs. Bichirs represent the earliest diverged living group of ray-finned fishes, and possess intriguing traits otherwise typical for lobe-finned fishes such as ventral paired lungs and larval external gills. In bichir embryos, we find that the anteroposterior way of formation of cranial segments is modified by the unique acceleration of the entire hyoid arch segment, with earlier and orchestrated development of the endodermal, mesodermal, and neural crest tissues. This major heterochronic shift in the anteroposterior developmental sequence enables early appearance of the external gills that represent key breathing organs of bichir free-living embryos and early larvae. Bichirs thus stay as unique models for understanding developmental mechanisms facilitating increased breathing capacity.

scholarly journals Norske drapsmenn (og kvinner) 1955-1982

2021 ◽  
Vol 108 (2) ◽  
pp. 360-379
Author(s):  
Hilde Dahl
Keyword(s):  
Research Field ◽  
Homicide Rate ◽  
The World ◽  
Historical Methods ◽  
Insight Into

Abstract:Homicides are rare in Norway; the country’s homicide rate is among the lowest in the world (UNODC, 2013). This might be why homicides always receive attention in the national news. The topic has also received attention on a governmental level. Reducing the number of homicides is an expressed goal in several official reports. However, preventive efforts require knowledge. While a handful of studies have been conducted using a variety of disciplinary approaches and methods, several recent reports point out that homicide is not a prioritized research field in Norway (NOU 2010:3; FHI rapport, 2012; JBD, 2018). This is the first article from the project »Homicides in Norway, 1955-1982, a historical-criminological study«. Studies using historical methods on homicide in the contemporary era have not previously been conducted in Norway. The projects aim is to provide historical insight into the rates and patterns of Norwegian homicide during the period 1955 to 1982, based on material originally collected by psychologist Ragnar Christensen (1922-2011) over the course of three decades.

scholarly journals Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species

2021 ◽  
Vol 12 ◽  
Author(s):  
Ola Alessa ◽  
Yoshitoshi Ogura ◽  
Yoshiko Fujitani ◽  
Hideto Takami ◽  
Tetsuya Hayashi ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Phylogenetic Relationship ◽  
Distinct Species ◽  
Genotypic Differences ◽  
Clade C ◽  
Single Genus ◽  
Almost All ◽  
Type Strains ◽  
Dependent Pathway ◽  
Insight Into

The pink-pigmented facultative methylotrophs (PPFMs), a major bacterial group found in the plant phyllosphere, comprise two genera: Methylobacterium and Methylorubrum. They have been separated into three major clades: A, B (Methylorubrum), and C. Within these genera, however, some species lack either pigmentation or methylotrophy, which raises the question of what actually defines the PPFMs. The present study employed a comprehensive comparative genomics approach to reveal the phylogenetic relationship among the PPFMs and to explain the genotypic differences that confer their different phenotypes. We newly sequenced the genomes of 29 relevant-type strains to complete a dataset for almost all validly published species in the genera. Through comparative analysis, we revealed that methylotrophy, nitrate utilization, and anoxygenic photosynthesis are hallmarks differentiating the PPFMs from the other Methylobacteriaceae. The Methylobacterium species in clade A, including the type species Methylobacterium organophilum, were phylogenetically classified into six subclades, each possessing relatively high genomic homology and shared phenotypic characteristics. One of these subclades is phylogenetically close to Methylorubrum species; this finding led us to reunite the two genera into a single genus Methylobacterium. Clade C, meanwhile, is composed of phylogenetically distinct species that share relatively higher percent G+C content and larger genome sizes, including larger numbers of secondary metabolite clusters. Most species of clade C and some of clade A have the glutathione-dependent pathway for formaldehyde oxidation in addition to the H4MPT pathway. Some species cannot utilize methanol due to their lack of MxaF-type methanol dehydrogenase (MDH), but most harbor an XoxF-type MDH that enables growth on methanol in the presence of lanthanum. The genomes of PPFMs encode between two and seven (average 3.7) genes for pyrroloquinoline quinone-dependent alcohol dehydrogenases, and their phylogeny is distinctly correlated with their genomic phylogeny. All PPFMs were capable of synthesizing auxin and did not induce any immune response in rice cells. Other phenotypes including sugar utilization, antibiotic resistance, and antifungal activity correlated with their phylogenetic relationship. This study provides the first inclusive genotypic insight into the phylogeny and phenotypes of PPFMs.

scholarly journals ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 70 ◽  
Author(s):  
Espen Mikal Robertsen ◽  
Hubert Denise ◽  
Alex Mitchell ◽  
Robert D. Finn ◽  
Lars Ailo Bongo ◽  
...  
Keyword(s):  
Environmental Samples ◽  
Genetic Material ◽  
Structure And Function ◽  
Marine Microbes ◽  
Exploration And Exploitation ◽  
Domain Specific ◽  
User Centric ◽  
Sustainable Services ◽  
And Function ◽  
Insight Into

Metagenomics, the study of genetic material recovered directly from environmental samples, has the potential to provide insight into the structure and function of heterogeneous microbial communities.  There has been an increased use of metagenomics to discover and understand the diverse biosynthetic capacities of marine microbes, thereby allowing them to be exploited for industrial, food, and health care products. This ELIXIR pilot action was motivated by the need to establish dedicated data resources and harmonized metagenomics pipelines for the marine domain, in order to enhance the exploration and exploitation of marine genetic resources. In this paper, we summarize some of the results from the ELIXIR pilot action “Marine metagenomics – towards user centric services”.

scholarly journals Marine Microbial Assemblages on Microplastics: Diversity, Adaptation, and Role in Degradation

2020 ◽  
Vol 12 (1) ◽  
pp. 209-232 ◽  
Author(s):  
Sonja Oberbeckmann ◽  
Matthias Labrenz
Keyword(s):  
Pathogenic Bacteria ◽  
Life Forms ◽  
Microbial Interactions ◽  
The Other ◽  
Human Society ◽  
Marine Microorganisms ◽  
Microbial Adaptation ◽  
Artificial Surfaces ◽  
Plastic Degradation

We have known for more than 45 years that microplastics in the ocean are carriers of microbially dominated assemblages. However, only recently has the role of microbial interactions with microplastics in marine ecosystems been investigated in detail. Research in this field has focused on three main areas: ( a) the establishment of plastic-specific biofilms (the so-called plastisphere); ( b) enrichment of pathogenic bacteria, particularly members of the genus Vibrio, coupled to a vector function of microplastics; and ( c) the microbial degradation of microplastics in the marine environment. Nevertheless, the relationships between marine microorganisms and microplastics remain unclear. In this review, we deduce from the current literature, new comparative analyses, and considerations of microbial adaptation concerning plastic degradation that interactions between microorganisms and microplastic particles should have rather limited effects on the ocean ecosystems. The majority of microorganisms growing on microplastics seem to belong to opportunistic colonists that do not distinguish between natural and artificial surfaces. Thus, microplastics do not pose a higher risk than natural particles to higher life forms by potentially harboring pathogenic bacteria. On the other hand, microplastics in the ocean represent recalcitrant substances for microorganisms that are insufficient to support prokaryotic metabolism and will probably not be microbially degraded in any period of time relevant to human society. Because we cannot remove microplastics from the ocean, proactive action regarding research on plastic alternatives and strategies to prevent plastic entering the environment should be taken promptly.

Trematodes and snails: an intimate association

2004 ◽  
Vol 82 (2) ◽  
pp. 251-269 ◽  
Author(s):  
Anne E Lockyer ◽  
Catherine S Jones ◽  
Leslie R Noble ◽  
David Rollinson
Keyword(s):  
Evolutionary History ◽  
Intermediate Hosts ◽  
Molecular Approaches ◽  
Complex Interactions ◽  
Intimate Association ◽  
In Vitro Cell Cultures ◽  
Medical Burden ◽  
Insight Into ◽  
Trematode Parasites

Trematode parasites share an intimate relationship with their gastropod intermediate hosts, which act as the vehicle for their development and transmission. They represent an enormous economic and medical burden in developing countries, stimulating much study of snail–trematode interactions. Laboratory-maintained snail–trematode systems and in vitro cell cultures are being used to investigate the molecular dialogue between host and parasite. These dynamic and finely balanced antagonistic relationships, in which parasites strongly influence the physiology of the host, are highly specific and may occasionally demonstrate co-speciation. We consider the mechanisms and responses deployed by trematodes and snails that result in compatibility or rejection of the parasite, and the macroevolutionary implications that they may effect. Although for gastropods the fossil record gives some insight into evolutionary history, elucidation of trematode evolution must rely largely upon molecular approaches, and for both, such techniques have provided fresh and often surprising evidence of their origins and dispersal over time. Co-evolution of snails and trematodes is becoming increasingly apparent at both cellular and population levels; the implications of which are only beginning to be understood for disease control. Untangling the complex interactions of trematodes and snails promise fresh opportunities for intervention to relieve the burden of parasitic disease.

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